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Yorodumi- PDB-2btn: Crystal Structure and Catalytic Mechanism of the Quorum-Quenching... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2btn | ||||||
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Title | Crystal Structure and Catalytic Mechanism of the Quorum-Quenching N- Acyl Homoserine Lactone Hydrolase | ||||||
Components | AIIA-LIKE PROTEIN | ||||||
Keywords | HYDROLASE / N-ACYL HOMOSERINE LACTONE HYDROLASE / QUORUM SENSING | ||||||
Function / homology | Function and homology information acyl-L-homoserine-lactone lactonohydrolase activity / quorum-quenching N-acyl-homoserine lactonase / metal ion binding Similarity search - Function | ||||||
Biological species | BACILLUS THURINGIENSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kim, M.H. / Choi, W.C. / Kang, H.O. / Lee, J.S. / Kang, B.S. / Kim, K.J. / Derewenda, Z.S. / Oh, T.K. / Lee, C.H. / Lee, J.K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: The Molecular Structure and Catalytic Mechanism of a Quorum-Quenching N-Acyl-L-Homoserine Lactone Hydrolase. Authors: Kim, M.H. / Choi, W.C. / Kang, H.O. / Lee, J.S. / Kang, B.S. / Kim, K.J. / Derewenda, Z.S. / Oh, T.K. / Lee, C.H. / Lee, J.K. #1: Journal: Biochim.Biophys.Acta / Year: 2005 Title: Crystallization and Preliminary Crystallographic Analysis of Bacillus Thuringiensis Ahl-Lactonase Authors: Kim, M.H. / Kang, H.O. / Kang, B.S. / Kim, K.J. / Choi, W.C. / Oh, T.K. / Lee, C.H. / Lee, J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2btn.cif.gz | 108.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2btn.ent.gz | 83.9 KB | Display | PDB format |
PDBx/mmJSON format | 2btn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2btn_validation.pdf.gz | 435.2 KB | Display | wwPDB validaton report |
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Full document | 2btn_full_validation.pdf.gz | 436.6 KB | Display | |
Data in XML | 2btn_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 2btn_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/2btn ftp://data.pdbj.org/pub/pdb/validation_reports/bt/2btn | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28496.514 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS THURINGIENSIS (bacteria) / Plasmid: PMAL-HIS-PARALLEL1/AIIA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ESCHERICHIA COLI XL1-BLUE / References: UniProt: Q7B8C3, UniProt: P0CJ63*PLUS | ||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE FIRST TWO RESIDUES IN THE SEQRES ARE FROM THE CLONING PROCEDURE RESULTING FROM THE RESTRICTION ...THE FIRST TWO RESIDUES IN THE SEQRES ARE FROM THE CLONING PROCEDURE RESULTING FROM THE RESTRICTIO | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35 % |
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Crystal grow | pH: 7.8 / Details: 0.1 M TRIS-HCL(PH 7.8), 30% PEG 4000,0.2 M MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.1271 |
Detector | Detector: CCD / Date: Nov 23, 2004 / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 2→44.6 Å / Num. obs: 15232 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.4 / % possible all: 97.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.63 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.632 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.92 Å2
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Refinement step | Cycle: LAST / Resolution: 2→44.63 Å
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